keep finding thousands of copies in random folders

After installing the last zimbra desktop release, which I use to sync with imap webmail service offered by godaddy, I started to notice random folders with thousands of email copies taking up multiple gigabytes of space. I went online to my webmail and deleted every message and deleted every message in zimbra desktop and emptied and purged trash and deleted messages and eventually I could get it to stop happening although I was deleting my email multiple times to make it stop.

Now I just looked in one of my folders and I have 24,975 messages in it that are mostly all copies of existing messages. I am getting really tired of this! Is there a fix? Why is this happening?